Complex systems

Software

  • epydemic, epidemic and other network processes in Python
  • epyc, computational experiment management in Python

Books

Publications

Peter Mann, V. Anne Smith, John Mitchell, and Simon Dobson. Symbiotic and antagonistic disease dynamics on clustered networks using bond percolation. Submitted to Physical Review E.

Simon Dobson. Epidemic modelling – Some notes, maths, and code. Independent Publishing Network, 2020. ISBN 978-183853-565-0. URL: https://simoninireland.github.io/introduction-to-epidemics/.

Peter Mann, V. Anne Smith, John Mitchell, and Simon Dobson. Two-pathogen model with competition on clustered networks. Physical Review E, 2021. To appear. URL: https://arxiv.org/abs/2007.03287.

Peter Mann, V. Anne Smith, John Mitchell, and Simon Dobson. Co-operative co-infection dynamics on clustered networks. Physical Review E, April 2021. URL: https://doi.org/10.1103/PhysRevE.103.042307.

Peter Mann, V. Anne Smith, John Mitchell, and Simon Dobson. Random graphs with arbitrary clustering and their applications. Physical Review E, January 2021. URL: https://doi.org/10.1103/PhysRevE.103.012309.

Peter Mann, V. Anne Smith, John Mitchell, and Simon Dobson. Percolation in random graphs with higher-order clustering. Physical Review E, January 2021. URL: https://doi.org/10.1103/PhysRevE.103.012313.

Michael Pitcher, Simon Dobson, Tom Kelsey, Mark Chaplain, Derek Sloan, Stephen Gillespie, and Ruth Bowness. How mechanistic in silico modelling can improve our understanding of TB disease and treatment. International Journal of Tuberculosis and Lung Disease, 2020. URL: https://doi.org/10.5588/ijtld.20.0107.

Michael Pitcher, Ruth Bowness, Simon Dobson, Raluca Eftimie, and Stephen Gillespie. Modelling the effects of environmental heterogeneity within the lung on the tuberculosis lifecycle. Journal of Theoretical Biology, June 2020. URL: https://dx.doi.org//10.1101/2019.12.12.871269.

Michael Pitcher, Ruth Bowness, Simon Dobson, and Stephen Gillespie. A spatially heterogeneous network-based metapopulation model applied to the simulation of a pulmonary tuberculosis infection. Applied Network Science, August 2018. URL: https://dx.doi.org//10.1007/s41109-018-0091-2.

Simon Dobson, Saray Shai, Emanuele Strano, and Marc Barthélemy. Multiplex cities: interacting transport networks in metropolitan areas. Presented at the SICSA Workshop on Modelling and Optimisation of Real-World Transportation, January 2015. URL: https://simondobson.org/softcopy/urban-networks-sicsa.pdf.

Michael Pitcher, Ruth Bowness, Simon Dobson, and Stephen Gillespie. A network-based metapopulation model to simulate a pulmonary tuberculosis infection. Poster at the 6th International Conference on Complex Networks and their Applications, November 2017.

Aleksejs Sazonovs, Simon Dobson, and Oscar Gaggiotti. A metapopulation model for predicting the success of genetic control measures for malaria. Poster at the SICSA Workshop on Computational Ecology, October 2015. URL: https://simondobson.org/softcopy/sazonovs-poster-15.pdf.

Simon Dobson. Exploring epidemic spreading using network models. Invited talk to the Institute of Mathematics and its Applications (North-West branch), December 2020. URL: https://simondobson.org/softcopy/exploring-epidemic-spreading.pdf.

Simon Dobson. A possible smeared phase transition in epidemic track-and-trace. School seminar, School of Computer Science, University of St Andrews, October 2020. URL: https://simondobson.org/softcopy/smeared-phase-transition.pdf.

Simon Dobson. Modelling urban networks: some results and their limitations. Talk in the Leeds Applied Nonlinear Dynamics seminar series, University of Leeds, March 2016. URL: https://simondobson.org/softcopy/urban-networks-16.pdf.

Simon Dobson. A complex cocktail of networks and reality. Presentation at the St Andrews Big Data and Discrete Mathematics Symposium, February 2016. URL: https://simondobson.org/softcopy/complex-cocktail.pdf.

Simon Dobson and Saray Shai. Complex networks and complex processes. Invited talk to the Department of Computer Science, University of York, March 2014. URL: https://simondobson.org/softcopy/complex-networks-complex-processes.pdf.